FMO DATABASE

FMODB ID: Z6ZVN

Calculation Name: 4K59-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4K59

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H2

Base Structure: X-ray

Registration Date: 2023-06-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptHSide
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	66
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-343002.285379
FMO2-HF: Nuclear repulsion	317901.535397
FMO2-HF: Total energy	-25100.749982
FMO2-MP2: Total energy	-25175.012043

3D Structure

Snapshot

Ligand structure

Ligand Interaction

Ligand binding energy

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
N/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)

Summations of interaction energy for fragment #1(A:3:ALA)

IFIE [kcal/mol]	PIEDA [kcal/mol]				Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level.	ESElectro static interaction energy.	EXExchange-repulsion energy.	CT+mixCharge transfer and mixing terms energy.	DI(MP2)Dispersion energy.	q(I=>J)Charge transfer value from I to J fragments.
-19.972	-21.618	22.506	-8.907	-11.955	-0.067

Interaction energy analysis for fragmet #1(A:3:ALA)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.047 / q_NPA : -0.039

Distance from base fragment(s) [Å]

Dist

Interaction energy by IFIE and PIEDA
[kcal/mol]

| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >

Fragment charge [e]

FCHARGE q_Mulliken
q_NPA q(I=>J)

Residue

Res # RES

Sort

Graph Options

X Axis Label
Y Axis Max Y Axis Min
Display ES EX CT+mix DI(MP2)

frag_NumFragment number.	ChainChain species.	Res #Residue number.	RES3-letter code of amino acid residue, ligand and solvent molecule.	FCHARGEFormal charge [e].	q_MullikenFragment charge evaluated by Mulliken charge [e].	q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e].	DISTDistance from Ligand [Å].	TotalIFIE at MP2 level [kcal/mol].	ESElectro static interaction energy by PIEDA [kcal/mol].	EXExchange-repulsion energy by PIEDA [kcal/mol].	CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol].	DI(MP2)Dispersion energy by PIEDA [kcal/mol].	q(I=>J)Charge transfer value from I to J fragmens [e].
3	A	5	GLY	0	-0.002	0.010	3.807	-1.736	-0.194	-0.024	-0.763	-0.755	0.002
4	A	6	PHE	0	0.015	-0.007	5.145	1.168	1.187	-0.001	-0.008	-0.010	0.000
5	A	7	LEU	0	0.012	0.012	7.517	-0.279	-0.279	0.000	0.000	0.000	0.000
6	A	8	ILE	0	0.015	0.009	10.317	0.032	0.032	0.000	0.000	0.000	0.000
7	A	9	LEU	0	-0.031	-0.008	12.845	-0.034	-0.034	0.000	0.000	0.000	0.000
8	A	10	SER	0	-0.019	0.005	16.034	-0.020	-0.020	0.000	0.000	0.000	0.000
9	A	11	ARG	1	0.733	0.830	17.626	-0.241	-0.241	0.000	0.000	0.000	0.000
10	A	12	ARG	1	0.876	0.921	20.530	-0.153	-0.153	0.000	0.000	0.000	0.000
11	A	13	GLU	-1	-0.891	-0.955	23.268	0.087	0.087	0.000	0.000	0.000	0.000
12	A	14	GLY	0	-0.025	-0.009	24.516	-0.001	-0.001	0.000	0.000	0.000	0.000
13	A	15	GLU	-1	-0.844	-0.891	22.046	0.181	0.181	0.000	0.000	0.000	0.000
14	A	16	GLY	0	0.025	0.010	19.092	-0.004	-0.004	0.000	0.000	0.000	0.000
15	A	17	ILE	0	-0.054	-0.033	13.511	0.014	0.014	0.000	0.000	0.000	0.000
16	A	18	THR	0	0.023	0.015	15.645	-0.016	-0.016	0.000	0.000	0.000	0.000
17	A	19	LEU	0	-0.034	-0.022	9.344	0.083	0.083	0.000	0.000	0.000	0.000
18	A	20	SER	0	-0.005	-0.005	11.920	-0.111	-0.111	0.000	0.000	0.000	0.000
19	A	21	LEU	0	0.012	0.006	10.286	0.163	0.163	0.000	0.000	0.000	0.000
20	A	22	LYS	1	0.842	0.922	9.649	-1.084	-1.084	0.000	0.000	0.000	0.000
21	A	23	ALA	0	0.018	0.007	13.458	-0.017	-0.017	0.000	0.000	0.000	0.000
22	A	24	ASP	-1	-0.912	-0.955	15.516	0.389	0.389	0.000	0.000	0.000	0.000
23	A	25	TYR	0	-0.059	-0.029	9.413	0.050	0.050	0.000	0.000	0.000	0.000
24	A	26	PRO	0	0.031	0.019	12.880	-0.021	-0.021	0.000	0.000	0.000	0.000
25	A	27	ALA	0	0.038	0.008	13.702	0.048	0.048	0.000	0.000	0.000	0.000
26	A	28	GLU	-1	-0.798	-0.910	13.301	0.216	0.216	0.000	0.000	0.000	0.000
27	A	29	GLU	-1	-0.908	-0.957	10.466	0.252	0.252	0.000	0.000	0.000	0.000
28	A	30	LEU	0	-0.025	0.002	8.422	0.115	0.115	0.000	0.000	0.000	0.000
29	A	31	ILE	0	-0.005	-0.001	8.401	0.068	0.068	0.000	0.000	0.000	0.000
30	A	32	ARG	1	0.861	0.919	9.672	-0.173	-0.173	0.000	0.000	0.000	0.000
31	A	33	GLN	0	0.021	0.006	4.592	0.210	0.266	-0.001	-0.007	-0.048	0.000
32	A	34	LEU	0	0.001	-0.011	5.276	-0.142	-0.142	0.000	0.000	0.000	0.000
33	A	35	ARG	1	0.891	0.949	6.435	-0.302	-0.302	0.000	0.000	0.000	0.000
34	A	36	GLU	-1	-0.996	-0.976	6.538	-0.102	-0.102	0.000	0.000	0.000	0.000
35	A	37	GLY	0	-0.043	-0.013	2.698	-0.669	-0.349	0.269	-0.245	-0.344	0.000
36	A	38	GLY	0	0.019	0.014	3.561	0.018	0.405	0.020	-0.113	-0.295	-0.002
37	A	39	ILE	0	-0.016	-0.021	3.159	-1.323	-0.111	0.075	-0.542	-0.745	-0.005
38	A	40	ARG	1	0.887	0.944	3.876	-0.077	0.078	-0.001	-0.016	-0.139	0.000
39	A	41	ILE	0	0.028	0.013	5.701	0.547	0.547	0.000	0.000	0.000	0.000
40	A	42	LEU	0	-0.014	-0.006	9.138	-0.221	-0.221	0.000	0.000	0.000	0.000
41	A	43	VAL	0	0.015	0.014	11.208	0.085	0.085	0.000	0.000	0.000	0.000
42	A	44	THR	0	-0.047	-0.037	12.445	-0.033	-0.033	0.000	0.000	0.000	0.000
43	A	45	ASP	-1	-0.851	-0.911	14.986	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	46	ILE	0	-0.023	-0.018	18.699	0.028	0.028	0.000	0.000	0.000	0.000
45	A	47	ILE	0	-0.009	-0.001	21.603	-0.013	-0.013	0.000	0.000	0.000	0.000
46	A	48	GLY	0	0.025	0.012	24.298	0.011	0.011	0.000	0.000	0.000	0.000
47	A	49	ASN	0	0.000	0.001	26.426	-0.006	-0.006	0.000	0.000	0.000	0.000
48	A	50	GLN	0	-0.014	-0.006	21.732	0.011	0.011	0.000	0.000	0.000	0.000
49	A	51	ALA	0	0.039	0.018	19.300	-0.019	-0.019	0.000	0.000	0.000	0.000
50	A	52	ARG	1	0.901	0.951	16.481	-0.032	-0.032	0.000	0.000	0.000	0.000
51	A	53	VAL	0	0.019	0.003	12.601	-0.037	-0.037	0.000	0.000	0.000	0.000
52	A	54	GLY	0	0.009	0.006	10.175	0.055	0.055	0.000	0.000	0.000	0.000
53	A	55	ILE	0	-0.028	-0.030	7.437	-0.085	-0.085	0.000	0.000	0.000	0.000
54	A	56	GLU	-1	-0.886	-0.933	1.849	-14.876	-18.285	15.139	-7.007	-4.722	-0.059
55	A	57	ALA	0	0.053	0.016	2.875	-0.820	0.267	0.379	-0.317	-1.150	0.002
56	A	58	PRO	0	0.064	0.023	2.402	-0.596	-1.995	6.508	-1.570	-3.538	-0.005
57	A	59	ARG	1	0.967	0.967	2.991	-0.155	-1.771	0.143	1.681	-0.209	0.000
58	A	60	GLY	0	0.039	0.025	6.494	-0.307	-0.307	0.000	0.000	0.000	0.000
59	A	61	VAL	0	-0.027	-0.001	6.168	-0.288	-0.288	0.000	0.000	0.000	0.000
60	A	62	LEU	0	-0.061	-0.030	8.151	0.107	0.107	0.000	0.000	0.000	0.000
61	A	63	ILE	0	0.009	-0.001	7.343	-0.046	-0.046	0.000	0.000	0.000	0.000
62	A	64	VAL	0	0.000	-0.003	11.605	-0.061	-0.061	0.000	0.000	0.000	0.000
63	A	65	ARG	1	0.879	0.936	15.395	-0.330	-0.330	0.000	0.000	0.000	0.000
64	A	66	ASP	-1	-0.780	-0.892	17.957	0.316	0.316	0.000	0.000	0.000	0.000
65	A	67	GLU	-1	-0.824	-0.876	20.723	0.251	0.251	0.000	0.000	0.000	0.000
66	A	68	LEU	0	-0.052	-0.009	19.570	-0.011	-0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:3:ALA)